7OAU | pdb_00007oau

Nanobody C5 bound to Kent variant RBD (N501Y)

X-RAY DIFFRACTION

---

Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	7OAO

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP		293	0.2 M Ammonium fluoride and 20 % Peg 3350

Crystal Properties
Matthews coefficient	Solvent content
2.19	43.92

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 28.81	α = 90
b = 153.73	β = 100.33
c = 75.85	γ = 90

Symmetry
Space Group	P 1 21 1

Diffraction

Diffraction Experiment
ID #	Crystal ID	Scattering Type	Data Collection Temperature	Detector	Detector Type	Details	Collection Date	Monochromator	Protocol
1	1	x-ray	100	PIXEL	DECTRIS PILATUS 6M		2021-03-21	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	DIAMOND BEAMLINE I24	0.9999	Diamond	I24

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	Rpim I (All)	CC (Half)	Net I Over Average Sigma (I)	Redundancy	Number Reflections (All)	Number Reflections (Observed)	Observed Criterion Sigma (F)	Observed Criterion Sigma (I)	B (Isotropic) From Wilson Plot
1	1.65	39	100	0.044	1	10	6.6		77705

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	Rpim I (All)	CC (Half)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	1.65	1.69	100		0.56	0.6	1.2	6

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	Starting model	Resolution (High)	Resolution (Low)	Number Reflections (Observed)	Number Reflections (R-Free)	Percent Reflections (Observed)	R-Factor (All)	R-Work (Depositor)	R-Work (DCC)	R-Free (Depositor)	R-Free (DCC)	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	FREE R-VALUE	7OAO	1.65	38.462	77679	3776	99.967	0.177	0.1754	0.18	0.1992	0.21	29.12

Temperature Factor Modeling
Anisotropic B[1][1]	Anisotropic B[1][2]	Anisotropic B[1][3]	Anisotropic B[2][2]	Anisotropic B[2][3]	Anisotropic B[3][3]
0.02		0.707	-2.163		1.768

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	31.749
r_dihedral_angle_4_deg	16.287
r_dihedral_angle_3_deg	11.56
r_dihedral_angle_1_deg	6.913
r_lrange_it	5.963
r_lrange_other	5.961
r_scangle_it	3.356
r_scangle_other	3.355
r_scbond_it	2.179
r_scbond_other	2.179
r_mcangle_it	1.893
r_mcangle_other	1.892
r_angle_refined_deg	1.337
r_angle_other_deg	1.323
r_mcbond_it	1.314
r_mcbond_other	1.314
r_nbd_refined	0.18
r_symmetry_nbd_other	0.173
r_nbtor_refined	0.168
r_symmetry_nbd_refined	0.159
r_nbd_other	0.159
r_xyhbond_nbd_refined	0.152
r_symmetry_xyhbond_nbd_refined	0.136
r_symmetry_nbtor_other	0.073
r_ncsr_local_group_2	0.064
r_chiral_restr	0.06
r_ncsr_local_group_1	0.056
r_bond_refined_d	0.007
r_gen_planes_refined	0.006
r_bond_other_d	0.001
r_gen_planes_other	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	4892
Nucleic Acid Atoms
Solvent Atoms	470
Heterogen Atoms	34

Software

Software
Software Name	Purpose
REFMAC	refinement
xia2	data reduction
xia2	data scaling
PHASER	phasing